| Raritan R SB (LongValley br to 74d44m15s) | NJ | Lake | Not Supporting | 4 | 12 |
| Raritan R SB (NB to Pleasant Run) | NJ | Lake | Not Supporting | 5 | 7.95 |
| Raritan R SB (Pleasant Run-Three Bridges) | NJ | Lake | Not Supporting | 4 | 0.91 |
| Raritan R SB (River Rd to Spruce Run) | NJ | Lake | Not Supporting | 4 | 1.24 |
| Raritan R SB (Spruce Run-StoneMill gage) | NJ | Lake | Not Supporting | 2 | 18 |
| Raritan R SB (Three Bridges-Prescott Bk) | NJ | Lake | Not Supporting | 6 | 1.63 |
| Reed Branch (Still Run) | NJ | Lake | Not Supporting | 2 | 58 |
| Reeds Bay / Absecon Bay & tribs | NJ | Lake | Not Supporting | 2 | 23 |
| Repaupo Ck (belowTomlin Sta Rd)/CedarSwamp | NJ | Lake | Not Supporting | 1 | 71 |
| Ridgeway Br (below Hope Chapel Rd) | NJ | Lake | Not Supporting | 4 | 1.53 |
| Ridgeway Br (Hope Chapel Rd to HarrisBr) | NJ | Lake | Not Supporting | 1 | 61 |
| Riggins Ditch (Moores Beach to East Pt) | NJ | Lake | Not Supporting | 2 | 1.79 |
| Ringwood Creek | NJ | Lake | Not Supporting | 2 | 13 |
| Robinsons Br Rahway R (below Lake Ave) | NJ | Lake | Not Supporting | 4 | 13 |
| Rock Brook (below Camp Meeting Ave) | NJ | Lake | Not Supporting | 1 | 8.73 |
| Rockaway Ck (below McCrea Mills) | NJ | Lake | Not Supporting | 4 | 14 |
| Rockaway Ck SB | NJ | Lake | Not Supporting | 5 | 25 |
| Rockaway R (74d 33m 30s to Stephens Bk) | NJ | Lake | Not Supporting | 2 | 17 |
| Rockaway R (above Longwood Lake outlet) | NJ | Lake | Not Supporting | 4 | 144 |
| Rockaway R (BM 534 brdg to 74d 33m 30s) | NJ | Lake | Not Supporting | 2 | 11 |
| Rockaway R (Boonton dam to Stony Brook) | NJ | Lake | Not Supporting | 6 | 799 |
| Rockaway R (Passaic R to Boonton dam) | NJ | Lake | Not Supporting | 7 | 2.78 |
| Rockaway R (Stephens Bk to Longwood Lk) | NJ | Lake | Not Supporting | 3 | 2.46 |
| Rockaway R (Stony Brook to BM 534 brdg) | NJ | Lake | Not Supporting | 4 | 132 |
| Rocky Brook (above Monmouth Co line) | NJ | Lake | Not Supporting | 1 | 16 |
| Rocky Brook (below Monmouth Co line) | NJ | Lake | Not Supporting | 6 | 39 |
| Royce Brook (above Branch Royce Brook) | NJ | Lake | Not Supporting | 3 | 4.03 |
| Russia Brook (above Milton) | NJ | Lake | Not Supporting | 2 | 82 |
| Russia Brook (below Milton) | NJ | Lake | Not Supporting | 3 | 67 |
| Saddle River (above Ridgewood gage) | NJ | Lake | Not Supporting | 4 | 19 |
| Saddle River (Hohokus to Ridgewood gage) | NJ | Lake | Not Supporting | 6 | 4.24 |
| Saddle River (Lodi gage to Rt 4) | NJ | Lake | Not Supporting | 6 | 4.40 |
| Saddle River (Rt 4 to Hohokus) | NJ | Lake | Not Supporting | 5 | 0.90 |
| Salem R (39-40-14 dam-CoursesLndg)/Canal | NJ | Lake | Not Supporting | 5 | 26 |
| Salem R (above Woodstown gage) | NJ | Lake | Not Supporting | 9 | 121 |
| Salem R (CountyHomeRd to Woodstown gage) | NJ | Lake | Not Supporting | 7 | 0.02 |
| Salem R (CoursesLanding to CountyHomeRd) | NJ | Lake | Not Supporting | 8 | 20 |
| Savages Run (above East Creek Pond) | NJ | Lake | Not Supporting | 2 | 27 |
| Scotland Run (above Fries Mill) | NJ | Lake | Not Supporting | 2 | 60 |
| Scotland Run (below Delsea Drive) | NJ | Lake | Not Supporting | 3 | 99 |
| Scotland Run (Delsea Drive to FriesMill) | NJ | Lake | Not Supporting | 2 | 51 |
| Second River | NJ | Lake | Not Supporting | 4 | 1.31 |
| Shabakunk Creek | NJ | Lake | Not Supporting | 8 | 33 |
| Shady Brook/Spring Lake/Rowan Lake | NJ | Lake | Not Supporting | 2 | 62 |
| Shallow Brook (Devils Brook) | NJ | Lake | Fully Supporting | 0 | 2.87 |
| Shannae Brook | NJ | Lake | Not Supporting | 2 | 158 |
| Shark River (below Remsen Mill gage) | NJ | Lake | Not Supporting | 8 | 3.71 |
| Shimers Brook | NJ | Lake | Not Supporting | 2 | 140 |
| Shipetaukin Creek | NJ | Lake | Not Supporting | 3 | 6.55 |
| Shrewsbury River (above Navesink River) | NJ | Lake | Not Supporting | 8 | 3.04 |