This work investigated the role of fertilizer application rate on phosphorus (P) transport and loading to Lake Uluabat in Turkey. For this purpose ArcView Interface of Soil and Water Assessment Tool 2000 (AVSWAT) was used. Results showed that when the fertilizer amount applied to agricultural lands was doubled, the P load to Lake Uluabat increased by 32%. P transported to Lake Uluabat declined by about 6, 10 and 16%, when the fertilizer usage at the agricultural fields were decreased by 20, 30 and 50%, respectively. In general, a linear relationship was observed between the P load and the fertilizer application rates. The highest and lowest P losses were from the com and wheat productions, respectively. 70% more P was carried to Lake Uluabat from com, wheat, and tomato fields when the fertilizer amounts applied were doubled. When the fertilizer usage declined by 20, 30, and 50%, a total of 14, 21 and 35% less P were transported to the lake from the fields, respectively. For the threshold P loading, 56 of 78 subbasins were critical when the fertilizer usage was doubled. For 50% reduction in the fertilizer application rate, the number of critical subbasins decreased to 46. Nevertheless, this decrease was not sufficient to meet the goal P loading to Lake Uluabat.