Meiofauna community attributes of the lower Bonny estuary was investigated under a pollution regime. This is germane because of the strategic importance of meiofauna in the food chain and the sustenance of any aquatic ecosystem. Five stations representing diverse land based activities such as refuse dump site, fuel depot, fishing-landing areas, residential housing and a station located up-stream (control) were chosen for investigation. The meiofauna samples were collected from sediments in three replicate spots per station per sampling months at low tide. Sediment samples were stirred through (63-212nm) meshes to separate meiofauna and organic debris. Meiofauna samples were processed by first washing Meiofauna through a sieve of fine mesh size made of silk material, in order to wash off formation and excess silt or mud. Meiofauna samples were sorted out and identified using standard keys. Result from field studies indicate that meiofauna population abundance and diversity varied slightly between stations and seasons. There was however, no established trend. Meiofauna were generally more abundant in the rainy season than in the dry season. In general, pollution indicator meiofaunal taxa were more in all stations except the control station; the increasing impact of pollutants in the river led to a rise in the relative abundance of r-strategist genera like Chromadora. We conclude that the application of meiofaunal indices can be a useful tool for assessing the environmental quality of estuarine ecosystems.