The effect of channel diversion in Ilog, Negros Occidental, was studied by comparing fish species abundance and species richness in the two river mouths, namely, Bungol Channel in Andulauan and Bocana in Lower Ilog River of the Ilog-Hilabangan River System. Data were collected for six months, from March to May 2011 for the dry season and from July to September 2011 for the wet season. Samples were collected using cast net and other indigenous gears in the locality. About 56 fish species belonging to 49 families were noted, and only three of these were introduced species. Fish species abundance was significantly different (t-test, p = 0.04), only in Bocana during the dry season. Nevertheless, fish species richness varied with season, as evidenced by the higher values observed in different river mouths. Tidal flow can significantly contribute to fish abundance and species richness, particularly during the dry season. Channel diversion with accompanying change in river discharge affected fish species abundance and species richness. These were modified further due to anthropogenic activities.