| Sixmile Run (above Middlebush Rd) | NJ | Lake | Not Supporting | 3 | 2.30 |
| Skit Branch (Batsto River) | NJ | Lake | Not Supporting | 2 | 3.00 |
| Sleeper Branch (Rt 206 to Tremont Ave) | NJ | Lake | Not Supporting | 2 | 17 |
| Slough Brook | NJ | Lake | Not Supporting | 3 | 1.10 |
| Sluice Creek | NJ | Lake | Not Supporting | 1 | 11 |
| South River (below 39d26m15s) | NJ | Lake | Not Supporting | 4 | 7.51 |
| South River (below Duhernal Lake) | NJ | Lake | Not Supporting | 9 | 23 |
| South Run (above 74d35m) (Ft Dix) | NJ | Lake | Not Supporting | 1 | 26 |
| Sparkill Brook | NJ | Lake | Not Supporting | 4 | 1.70 |
| Sparta Junction tribs | NJ | Lake | Not Supporting | 7 | 115 |
| Spring Lake Fork of Bound Brook | NJ | Lake | Not Supporting | 5 | 6.45 |
| Springers Brook / Deep Run | NJ | Lake | Not Supporting | 3 | 51 |
| Spruce Run (above Glen Gardner) | NJ | Lake | Not Supporting | 2 | 6.17 |
| Spruce Run Reservior / Willoughby Brook | NJ | Lake | Not Supporting | 3 | 35 |
| Stephen Creek (GEHR) | NJ | Lake | Not Supporting | 5 | 59 |
| Still Run (above Silver Lake Road) | NJ | Lake | Not Supporting | 1 | 69 |
| Still Run (WillowGroveLk - SilverLakeRd) | NJ | Lake | Not Supporting | 3 | 36 |
| Still Run/London Br(above Tomlin Sta Rd) | NJ | Lake | Not Supporting | 4 | 24 |
| Stone House Brook | NJ | Lake | Not Supporting | 2 | 147 |
| Stony Bk (74d 48m 10s to 74d 49m 15s) | NJ | Lake | Not Supporting | 4 | 4.84 |
| Stony Bk (74d46m dam to/incl Baldwins Ck) | NJ | Lake | Not Supporting | 1 | 31 |
| Stony Bk (above 74d 49m 15s) | NJ | Lake | Not Supporting | 3 | 11 |
| Stony Bk (Baldwins Ck to 74d 48m 10s) | NJ | Lake | Not Supporting | 2 | 9.34 |
| Stony Bk (Harrison St to Rt 206) | NJ | Lake | Not Supporting | 4 | 0.03 |
| Stony Bk (Province Line Rd to 74d46m dam) | NJ | Lake | Not Supporting | 3 | 53 |
| Stony Bk (Rt 206 to Province Line Rd) | NJ | Lake | Not Supporting | 3 | 7.06 |
| Stony Bk- Princeton drainage | NJ | Lake | Not Supporting | 4 | 78 |
| Stony Brook (Boonton) | NJ | Lake | Not Supporting | 5 | 226 |
| Stony Brook (incl UDRV) | NJ | Lake | Not Supporting | 1 | 1.69 |
| Stony Brook (North Plainfield) | NJ | Lake | Not Supporting | 3 | 11 |
| Stow Creek (above Jericho Road) | NJ | Lake | Not Supporting | 1 | 31 |
| Swartswood Lake and tribs | NJ | Lake | Not Supporting | 6 | 634 |
| Swartswood trib(41-06-06 thru Lk Owassa) | NJ | Lake | Not Supporting | 3 | 175 |
| Swede Run | NJ | Lake | Not Supporting | 5 | 28 |
| Swimming River Reservior / Slope Bk | NJ | Lake | Not Supporting | 6 | 22 |
| Tenakill Brook | NJ | Lake | Not Supporting | 7 | 7.38 |
| Third River | NJ | Lake | Not Supporting | 10 | 4.73 |
| Three Pond Branch (Hospitality Branch) | NJ | Lake | Not Supporting | 1 | 1.60 |
| Toms R Estuary | NJ | Lake | Not Supporting | 8 | 54 |
| Toms River (74-22-30 rd to FrancisMills) | NJ | Lake | Not Supporting | 2 | 12 |
| Toms River (Hope Chapel Rd to Bowman Rd) | NJ | Lake | Not Supporting | 1 | 196 |
| Trout Brook | NJ | Lake | Not Supporting | 2 | 64 |
| Trout Brook / Lake Tranquility | NJ | Lake | Not Supporting | 5 | 130 |
| Troy Brook (above Reynolds Ave) | NJ | Lake | Not Supporting | 4 | 353 |
| Troy Brook (below Reynolds Ave) | NJ | Lake | Not Supporting | 2 | 23 |
| Tuckahoe River (39d19m52s to Cumberland Ave) | NJ | Lake | Not Supporting | 1 | 6.59 |
| Tuckahoe River (above Cumberland Ave) | NJ | Lake | Not Supporting | 1 | 14 |
| Tuckahoe River (below Rt 49) | NJ | Lake | Not Supporting | 2 | 8.96 |
| Tuckahoe River (lower) | NJ | Lake | Not Supporting | 1 | 8.45 |
| Tuckerton Creek (below Mill Branch) | NJ | Lake | Not Supporting | 4 | 28 |