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994-acre Port Jefferson Harbor fishing map with NOAA BlueTopo survey contours (98.97% measured, 99.86% assessed), charted rock and wreck structure, regional fish-survey occurrence, sourced forage timing and verified public access. The water tops out around 51 ft. The depth chart is built from real agency bathymetry referenced to NAVD88; directly measured coverage remains distinguished from source interpolation. The channels, holes and drop-offs come from the source data, not a distance-from-shore model. Below is the species-by-species picture, pulled from the same data the map uses.
Drawn out, this is 993 acres of water rimmed by 10 miles of bank, broken up by 2 islands. With a shoreline index of 2.3, this water is all arms and coves — edge habitat well beyond its acreage. Littoral water — the productive band under ~15 ft — makes up 28% of this chart. Call it 2.5 mi long by 1.5 mi wide at the broadest reach. For a second option, Setauket Harbor lies 1 mi southwest.
Early season striped bass use the shallows, holding in 5 to 20 ft. Summer is a 15 to 51 ft game here, winter a 20 to 50 ft one. The chart's best answer is Surveyed channel edge — drop-off, 29 ft, good for summer. Best bite is early morning and the evening. Tie on a topwater walker at low light or a paddletail on a light jig and you're in the game.
Depth note: when a documented seasonal range extends below this chart, the table shows the deepest mapped working water, not a verified holding depth.
| Season | Depth | Best window | Start at | Go-to baits |
|---|---|---|---|---|
| Spring | 5 to 20 ft | dawn & dusk | Surveyed channel edge (20 ft) | 3-6 inch paddletail, Suspending minnow plug |
| Summer | 15 to 51 ft chart-limited; documented 25 to 60 ft | dawn & dusk | Surveyed channel edge (29 ft) | Topwater walker at low light, Paddletail on a light jig |
| Fall | 10 to 35 ft | dawn & dusk | Surveyed channel edge (29 ft) | Pencil popper, Baitfish swimbait |
| Winter | 20 to 50 ft | midday | Surveyed channel edge (29 ft) | Slow paddletail, Bucktail near bottom |
In spring, bluefish run shallow here, mostly 3 to 20 ft. Summer pushes them deeper, 5 to 30 ft, and winter fish settle into 15 to 40 ft. Surveyed channel edge is the standout, a drop-off at roughly 29 ft, rated good for summer bluefish. Time it for early morning and the evening. You won't need more than a popper (early/late) or a metal jigs in the rips most summer days.
| Season | Depth | Best window | Start at | Go-to baits |
|---|---|---|---|---|
| Spring | 3 to 20 ft | dawn & dusk | Shallow feeding flat (19 ft) | Metal (Hopkins/Kastmaster), Pencil popper |
| Summer | 5 to 30 ft | dawn & dusk | Surveyed channel edge (29 ft) | Popper (early/late), Metal jigs in the rips |
| Fall | 3 to 25 ft | dawn & midday | Shallow feeding flat (19 ft) | Pencil popper, Big metal |
| Winter | 15 to 40 ft | midday | open water | Metal jig worked slow (southern waters) |
Spring summer flounder (fluke) on Port Jefferson Harbor hold shallow, usually 5 to 25 ft. By summer they slide out to 8 to 35 ft, and by winter most fish are in 15 to 51 ft. The chart's best answer is Surveyed channel edge — drop-off, 29 ft, prime for summer. Prime time lands in midday and early morning. The summer box starts with a bucktail (1-3 oz by drift speed) or a gulp grub on jighead.
Depth note: when a documented seasonal range extends below this chart, the table shows the deepest mapped working water, not a verified holding depth.
| Season | Depth | Best window | Start at | Go-to baits |
|---|---|---|---|---|
| Spring | 5 to 25 ft | midday & dawn | Surveyed channel edge (25 ft) | Bucktail + Gulp swimming mullet, Hi-lo rig + squid strip |
| Summer | 8 to 35 ft | midday & dawn | Surveyed channel edge (29 ft) | Bucktail (1-3 oz by drift speed), Gulp grub on jighead |
| Fall | 12 to 45 ft | midday | Surveyed channel edge (29 ft) | Heavier bucktail on the lumps, Big Gulp 6" grub |
| Winter | 15 to 51 ft chart-limited; documented 20 to 60 ft | midday | Surveyed channel edge (29 ft) | Slow bottom rig + strip |
Early season black sea bass use the shallows, holding in 10 to 40 ft. Summer is a 13 to 51 ft game here, winter a 15 to 51 ft one. The chart's best answer is NOAA charted underwater rock — rock pile, 14 ft, prime for spring. Best bite is midday and early morning. Tie on a bucktail + grub or a diamond jig + squid teaser and you're in the game.
Depth note: when a documented seasonal range extends below this chart, the table shows the deepest mapped working water, not a verified holding depth.
| Season | Depth | Best window | Start at | Go-to baits |
|---|---|---|---|---|
| Spring | 10 to 40 ft | midday & dawn | NOAA charted underwater rock (14 ft) | Hi-lo rig + squid, 1-2 oz bucktail + Gulp |
| Summer | 13 to 51 ft chart-limited; documented 15 to 60 ft | midday & dawn | NOAA charted underwater rock (14 ft) | Bucktail + grub, Diamond jig + squid teaser |
| Fall | 13 to 51 ft chart-limited; documented 20 to 80 ft | midday | NOAA charted underwater rock (14 ft) | 3-4 oz vertical jig (deep), Double-teaser rig |
| Winter | 15 to 51 ft chart-limited; documented 40 to 100 ft | midday | NOAA charted underwater rock (14 ft) | Heavy hi-lo rig on deep wrecks |
Start shallow in spring: tautog (blackfish) sit in 5 to 25 ft that time of year. Warm water sends them out to 10 to 35 ft; cold water stacks them in 15 to 51 ft. Top water on the chart: Dangerous NOAA charted wreck, a wreck in the 22 ft range, prime in spring. Fish it in early morning and you'll meet the bite. Throw a 1/2-1 oz tog jig + crab until the fish tell you otherwise.
Depth note: when a documented seasonal range extends below this chart, the table shows the deepest mapped working water, not a verified holding depth.
| Season | Depth | Best window | Start at | Go-to baits |
|---|---|---|---|---|
| Spring | 5 to 25 ft | midday & dawn | Dangerous NOAA charted wreck (22 ft) | Tog jig + green crab half, Bare jig + clam (early) |
| Summer | 10 to 35 ft | dawn | Dangerous NOAA charted wreck (35 ft) | 1/2-1 oz tog jig + crab |
| Fall | 10 to 50 ft | midday | Dangerous NOAA charted wreck (35 ft) | Tog jig + whole green crab, Old-school rig + double crab (deep) |
| Winter | 15 to 51 ft chart-limited; documented 30 to 70 ft | midday | Dangerous NOAA charted wreck (35 ft) | Heavy jig + crab on deep structure |
Spring scup (porgy) on Port Jefferson Harbor hold shallow, usually 5 to 25 ft. They move out to 6 to 35 ft in summer and finish the year down in 12 to 50 ft. Put NOAA charted underwater rock first on the milk run — a rock pile near 6 ft that grades prime for spring. The feeding windows run midday and early morning. The summer box starts with a hi-lo porgy rig or a micro metal jig.
| Season | Depth | Best window | Start at | Go-to baits |
|---|---|---|---|---|
| Spring | 5 to 25 ft | dawn | NOAA charted underwater rock (6 ft) | Small hi-lo rig, Micro jig tipped with bait |
| Summer | 6 to 35 ft | midday & dawn | NOAA charted underwater rock (6 ft) | Hi-lo porgy rig, Micro metal jig |
| Fall | 8 to 40 ft | midday | NOAA charted underwater rock (14 ft) | Compact vertical jig, Hi-lo rig |
| Winter | 12 to 50 ft | midday | NOAA charted underwater rock (14 ft) | Small slow vertical jig |
Port Jefferson Harbor also holds winter flounder (8 to 30 ft in summer). Pick any of them on the map above for rated spots and bait picks.
21 pieces of structure are mapped here — Dangerous NOAA charted wreck, around 35 ft, is the deepest of them.
Access data: New York State DEC — Boat Launches (FishNY). Confirm conditions and fees locally before you launch.
Season dates, license requirements, and size and bag limits for New York waters are set by the New York DEC (saltwater fishing) — and special regulations can apply to Port Jefferson Harbor specifically, so confirm the current rules before you fish.
Check the official New York fishing regulations →
Port Jefferson Harbor is about 51 ft (16 m) deep at its deepest point. The depth chart is built from real agency bathymetry referenced to NAVD88; directly measured coverage remains distinguished from source interpolation. The contours reflect measured and quality-assessed source depths.
Anglers target striped bass, bluefish, summer flounder (fluke), black sea bass, tautog (blackfish), scup (porgy), winter flounder on Port Jefferson Harbor. The list combines the water's survey records with habitat-filtered species from broader official evidence; those additions are plausible occurrences, not exact-water abundance or guaranteed catches.
NOAA charted underwater rock is the top-rated area: a rock pile in about 14 ft of water that rates prime for black sea bass in spring. Every other rated spot, per species and season, is on the map above.
For striped bass, the summer bite is best in early morning and the evening. Each species page section below lists the seasonal windows, and the map shows a live NOW badge when you're inside one.
Fishing on Port Jefferson Harbor is regulated by the New York DEC (saltwater fishing). Check the official New York regulations for current license requirements, season dates, and size and bag limits — special regulations can apply to this specific water.
Setauket Harbor 1 mi · Mount Sinai Harbor 3 mi · Smithtown Bay 6 mi · Lake Ronkonkoma 9 mi · Artist Lake 10 mi · Blydenburgh Lake 11 mi · Deep Pond 13 mi · Black Rock Harbor 15 mi, CT · Frash Pond 15 mi, CT · Northport Bay 15 mi · Centerport Harbor 16 mi · Knapps Lake 17 mi
See how Port Jefferson Harbor stacks up: best striped bass lakes in New York · best summer flounder (fluke) lakes in New York · best winter flounder lakes in New York · best bluefish lakes in New York
Browse all New York fishing maps. See every water on DepthScout. Bathymetry credit: NOAA BlueTopo (NAVD88; 99% measured, 1% source-interpolated). How we build these maps. Fish here with a sonar unit that logs? Send us your depth data and we'll improve this chart, credited to you. For fishing guidance only, never navigation.