Benthic macroinvertebrates have become popular for use in biological monitoring programs. Many of these organism’s life cycles are highly variable due to environmental conditions. Therefore it is important to understand how seasonal variability influences biological measurements of macroinvertebrate community structures (known as metrics) and how these influences may affect habitat water quality assessment. The reference stream Burris Fork in Moniteau county Missouri was sampled for benthic macroinvertebrates, water quality, and habitat parameters monthly from December, 2002 to December, 2003. A suite of 98 metrics, including 46 maturity weighted metrics, were calculated. The coefficient of variation of each metric was calculated as a means of showing how variable each metric can be during a single year. Models were constructed for each metric based on water quality and environmental parameters. Each model was evaluated by the mean square prediction error of 3 random sampling dates of the following year. Reduced and non-reduced sets of metrics were used for cluster analysis of sampling dates as a means of evaluating if community measures could adequately group seasonal periods. The importance of this work reveals that some metrics are less variable and thus preferable for assessing habitat quality in the region this study was conducted. Furthermore, it is important to understand that single snapshots of the macroinvertebrate community may not adequately characterize the health of streams systems.