The population dynamics of the estuarine isopod, Exosphaeroma hylocoetes, was investigated monthly from February 2006 to August 2007 in three temporarily open/closed Eastern Cape estuaries, the East and West Kleinemonde and Kasouga Estuaries. Mean isopod abundances and biomasses ranged between 0 and 4791 ind/m² and 0 and 9.65 mg/dwt/m² in the West Kleinemonde Estuary and between 0 and 108 ind/m² and 0 and 0.318 mg/dwt/m² in the nearby East Kleinemonde Estuary. In the Kasouga Estuary, the values ranged between 0 and 3650 ind/m² and 0 and 5.105 mg/dwt/m². Temporal changes in the abundance and biomass of E. hylocoetes within the three systems was primarily linked to mouth phase, with populations crashing when the mouth was open and to a lesser extent, seasonality. In all three estuaries maximum abundance and biomass was recorded in the middle reaches, which could be ascribed to the presence of submerged macrophytes. E. hylocoetes demonstrates strong sexual dimorphism, with males being significantly larger than females (P < 0.05). Sex ratios were skewed in favour of females in all three estuaries. Females were encountered carrying young from an overall length of 2.5 mm throughout the year