Coastal ecosystems continue to come under increasing pressure from human activities and the input of anthropogenic substances. This is being realised in a number of areas where eutrophic conditions begin to dominate and phenomena such as toxic algal blooms increase in frequency. Amidst this situation there is a growing need to understand how ecosystem components such as benthic fauna might respond to these conditions and how we might better use some of these components as indicators of ecosystem perturbation. In this context the current study examines the distribution and abundance of sediment meiofauna in seagrass beds at two different locations in Moreton Bay estuary. This ecosystem presently receives significant anthropogenic inputs from the Brisbane River and other sources draining the greater Brisbane catchment and adjoining areas. The main aims of the study were to characterise the distribution and abundance of meiofauna in these sediments and to also examine some of the main factors influencing these features. Also, it was intended that on examination be made of the influence that blooms of the cyanobacterium Lyngbya majuscula might have on meiofauna abundance and distribution in these areas. Blooms of this alga are an increasing feature of the Moreton Bay estuary and potentially represent a strong influence on a range of habitats and organisms within the ecosystem. In considering the physico-chemical aspects influencing meiofauna, sediment grain size and nutrient levels were shown to have some effect on distribution and abundance although this varied between species and location. Further, the grain size of the sediment and the total organic carbon did not change significantly between bloom and non-bloom periods and but total nitrogen and C/N ratio did show a change. In regard to the observed effects of the L. majuscula blooms, a negative impact was observed on copepod and nematode abundance and distribution. In both cases their abundance was considerably smaller during the bloom period. Notably, polychaetes showed no effect from the bloom?s occurrence. The results also indicate that during the bloom the meiofauna were distributing shallower in the sediment, probably due to the hypoxic conditions that the bloom may have created. Moreover, the impact of the bloom was more pronounced in the smaller size classes for the meiofauna and suggests that these classes are more sensitive to the conditions generated by the deposited bloom material. Under Multiple Regression Analysis nematodes and polychaetes were positively correlated with sediment nitrogen concentration, while copepods were not. Also, during the bloom the nitrogen concentration in the sediment increased but the abundance of nematodes showed an opposite trend. The general negative effect of the bloom on the total fauna might be the responsible for this result. An attempt was also made to assess whether the nematode:copepod ratio (Ne:Co) could be used in this ecosystem as an indicator of pollutant input or habitat disturbance by the algal bloom. This ratio has been used elsewhere with some success. Results from this study indicated that this ratio has only limited value as an indicator in the study situation and that the concomitant influence of sediment grain size and nutrient levels lead to a potentially misleading interpretation of the results that the ratio provides. The interactions between meiofauna, the prevailing physico-chemical and biological characteristics of the sediments in Moreton Bay are clearly very complex. The influence of phenomena such as the Lyngbya blooms adds to this complexity but, in the current study, this was seen to clearly have an effect on both animal abundance and their distribution. In this regard, the present study has identified the key areas of influence from the algal blooms and has also highlighted the need to further research these important animal groups so that we may better understand how the benthos, and thus the wider ecosystem, might cope with pollutants and anthropogenic disturbances.