Intermittently open/closed coastal lakes and lagoons (ICOLLs) are common in Australia. Isolation from the sea makes them susceptible to nutrient enrichment and pollution and many are considered degraded. Understanding of their ecology and the effects of anthropogenic activity is limited. Many lakes are kept open artificially to improve water quality and mitigate the effects of floods. The present study examined the relationship between multivariate and univariate patterns in higher taxa of meiobenthos and compared their densities and distributions in naturally open and closed lakes with those in managed lakes. The degree of correspondence between multivariate and univariate patterns was taxon and locality dependent. Differences in densities between types of lakes was not related to physical factors. Within lakes, meiobenthos generally correlated negatively with salinity and organic content, but positively with silt. Densities reflected the degree of isolation from the sea, but the influence of this factor varied among lakes within categories and between taxa. Most taxa were less abundant in isolated localities, such as the inner reaches of lakes and in closed lakes. Meiobenthos were more spatially variable in closed and in managed lakes. The influence of frequency and duration of closure on the ecology of coastal lakes is discussed.