Onchocerciasis is a widespread disease in intertropical Africa, which, ultimately, causes irreversible blindness. The disease is transmitted by a small blackfly, Simulium damnosum (Diptera), which has aquatic larval and pupal stages. The breeding sites of the blackflies are riffles. These river reaches are the targets of the control campaign of the Onchocerciasis Control Programme in West Africa (OCP). An aquatic monitoring network covering the totality of the area exposed to the insecticide was set up to evaluate environmental impact. In this paper, we present results from the OCP 20-year period of monitoring of the ichthyofauna regularly exposed to larvicides. We do not record any measurable effects of pesticides on the CPUE, abundance of species, trophic structure, community structure or fish health. However, we detect the emergence of a number of medium-term tendencies. These tendencies may relate to climatic conditions that have a consequent effect on hydrology. Thus, we note a constant decrease in the CPUE from the beginning of the monitoring until 1995. The rivers were treated during that time until 1990 or 1993, depending on the station. But even after the treatments ended, the number of catches continued to decrease. As a result, we consider other factors to be the cause of that decline. The average level of annual discharges in this region has been decreasing regularly from the beginning of the 1970s. The production of fish fluctuates in all the rivers according to the flood rate. Important floods inundate larger areas, making greater quantities of food available, and thus improving the conditions for reproduction. The determining factor of the ichthyological stock abundance seems to depend both on the extent and the duration of the flood. In our catches, the observed effect was not immediately evident but appeared a few years later as a cumulative effect of poor hydrological conditions. An increase in the CPUE since 1996 has been related to improved hydrological conditions. In these last few years, we have observed an intensification of the basic flow leading to a ground water renewal. Furthermore, on three of the stations investigated, it appeared that the impediment of rivers (dams) could induce different and/or antagonistic effects. In some cases, we have observed that in spite of unfavourable hydrological conditions, certain species appear to be favoured by the presence of the dam. But, the damming of the river has a negative effect on other species, particularly on the coefficient of condition of migratory fishes. The impact of these factors is enhanced by the fact they exist conjointly.