Final Tables 2008/2009
| DIVISION ONE | P | W | D | L | F | A | GD | Pts | |
| 1 | WEST KIRBY | 28 | 18 | 6 | 4 | 77 | 34 | 43 | 60 |
| 2 | UPTON ATHLETIC ASSOC. | 28 | 17 | 5 | 6 | 51 | 40 | 11 | 56 |
| 3 | POULTON VICTORIA | 28 | 16 | 6 | 6 | 55 | 23 | 32 | 54 |
| 4 | RUNCORN TOWN | 28 | 14 | 8 | 6 | 69 | 35 | 34 | 50 |
| 5 | NEWTON | 28 | 15 | 5 | 8 | 56 | 41 | 15 | 50 |
| 6 | CASTROL SOCIAL | 28 | 15 | 3 | 10 | 41 | 38 | 3 | 48 |
| 7 | CAMMELL LAIRD RES. | 28 | 14 | 4 | 10 | 67 | 40 | 27 | 46 |
| 8 | MAGHULL | 28 | 12 | 5 | 11 | 51 | 53 | -2 | 41 |
| 9 | MARINE RES. | 28 | 11 | 6 | 11 | 47 | 48 | -1 | 39 |
| 10 | ELLESMERE PORT | 28 | 11 | 5 | 12 | 48 | 46 | 2 | 38 |
| 11 | HESWALL | 28 | 9 | 6 | 13 | 42 | 62 | -20 | 33 |
| 12 | *VAUXHALL MOTORS RES. | 28 | 9 | 6 | 13 | 41 | 61 | -20 | 30 |
| 13 | CHRISTLETON | 28 | 6 | 5 | 17 | 35 | 56 | -21 | 23 |
| 14 | *HALTON | 28 | 4 | 3 | 21 | 33 | 73 | -40 | 12 |
| 15 | BLACON YOUTH CLUB | 28 | 1 | 3 | 24 | 25 | 88 | -63 | 6 |
| 16 | AINTREE VILLA RECORD EXPUNGED PER RULE 12 [C] | ||||||||
| DIVISION THREE | P | W | D | L | F | A | GD | Pts | |
| 1 | F.C.PENSBY | 30 | 22 | 4 | 4 | 64 | 28 | 36 | 70 |
| 2 | MARSHALLS | 30 | 18 | 5 | 7 | 98 | 42 | 56 | 59 |
| 3 | RUNCORN TOWN RES. | 30 | 16 | 7 | 7 | 74 | 49 | 25 | 55 |
| 4 | CHRISTLETON RES. | 30 | 14 | 10 | 6 | 62 | 39 | 23 | 52 |
| 5 | RICHMOND R.R.JACOBS | 30 | 13 | 11 | 6 | 56 | 38 | 18 | 50 |
| 6 | HALE | 30 | 14 | 7 | 9 | 74 | 46 | 28 | 49 |
| 7 | UPTON A.A. RES. | 30 | 14 | 5 | 11 | 62 | 58 | 4 | 47 |
| 8 | ASHVILLE RES. | 30 | 11 | 11 | 8 | 57 | 49 | 8 | 44 |
| 9 | CAPENHURST VILLA RES. | 30 | 12 | 7 | 11 | 57 | 50 | 7 | 43 |
| 10 | MERSEY ROYAL | 30 | 11 | 6 | 13 | 62 | 60 | 2 | 39 |
| 11 | *MANOR ATHLETIC | 30 | 11 | 5 | 14 | 65 | 64 | 1 | 35 |
| 12 | ELLESMERE PORT RES. | 30 | 8 | 9 | 13 | 56 | 74 | -18 | 33 |
| 13 | SOUTHPORT TRINITY RES. | 30 | 8 | 5 | 17 | 42 | 78 | -36 | 29 |
| 14 | *FOCUS | 30 | 8 | 5 | 17 | 53 | 94 | -41 | 26 |
| 15 | *ST WERBURGHS | 30 | 5 | 6 | 19 | 53 | 97 | -44 | 18 |
| 16 | BLACON YOUTH CLUB RES. | 30 | 2 | 3 | 25 | 32 | 101 | -69 | 9 |