LRunkle's right, the most accurate way to do it is to take a rag tape, stretch it tight and level across your creek and use a survey rod or yard stick and take a depth at each increment, usually 1'. Figure out how high your tape is above the average water level and subtract it from each of your depth readings.
You can then plot it in cad, or on graph paper to be highly accurate. Even easier is to just add all the depths and divide by the count and multiply by the width of the creek to get an average end area of that crossing.
Erich