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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, Mount Sinai Harbor lies 3 mi east.
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, prime for summer. Best bite is early morning and the evening. Tie on a flutter spoon (deep) or an umbrella rig (trolled) and you're in the game.
| Season | Depth | Best window | Start at | Go-to baits |
|---|---|---|---|---|
| Spring | 5 to 20 ft | dawn & dusk | Surveyed channel edge (20 ft) | Bucktail jig + trailer, Walking topwater (dawn) |
| Summer | 15 to 51 ft | dawn & dusk | Surveyed channel edge (29 ft) | Flutter spoon (deep), Umbrella rig (trolled) |
| Fall | 10 to 35 ft | dawn & dusk | Surveyed channel edge (29 ft) | Topwater walker, Jerkbait |
| Winter | 20 to 50 ft | midday | Surveyed channel edge (29 ft) | Alabama rig (slow), Flutter spoon |
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 prime 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 | Surveyed channel edge (29 ft) | 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.
| 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 | 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.
| 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 | midday & dawn | NOAA charted underwater rock (14 ft) | Bucktail + grub, Diamond jig + squid teaser |
| Fall | 13 to 51 ft | midday | NOAA charted underwater rock (14 ft) | 3-4 oz vertical jig (deep), Double-teaser rig |
| Winter | 15 to 51 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.
| 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 | midday | Dangerous NOAA charted wreck (35 ft) | Heavy jig + crab on deep structure |
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) on Port Jefferson Harbor.
Surveyed channel edge is the top-rated area: a drop-off in about 29 ft of water that rates prime for summer flounder (fluke) in summer. 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.
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 · Frash Pond 15 mi, CT · Northport Bay 15 mi · Centerport Harbor 16 mi · Knapps Lake 17 mi · Cockenoe Harbor 17 mi, CT · Huntington Bay 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 bluefish lakes in New York · best black sea bass lakes in New York
Browse all New York fishing maps or 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.