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The seasonal dynamics and spatial variability of macroinvertebrate assemblages in Alpine streams are becoming better understood. However, the implications of this knowledge for indices used in monitoring programs have yet to be fully considered. Establishing the ecological status of such streams using macroinvertebrates may then be difficult if what is expected to be found, and where, varies across small distances between streams at a given altitude, or between years in response to different climatic characteristics. In this paper, we evaluated the degree of spatial variability in macroinvertebrate abundance and diversity for 14 tributaries at similar altitude that feed a 6-km reach of an Alpine stream, and how this spatial variability differs within and between years. Environmental variables and macroinvertebrates were sampled on 10 dates for assessment. The data showed that differences in environmental characteristics over relatively short distances lead to between tributary differences in the windows of opportunity and hence when a tributary should be sampled for monitoring purposes. Superimposed on this spatial variability was inter-annual variability linked to climate differences that shifted this window of opportunity in time, and thus altered when monitoring was optimal for any one tributary in any one year. If biological indices are not rendered sensitivity to these variations, the results obtained may reflect more natural variability than possible human impacts.