Three different approaches may be taken to a wetland analysis, based largely on the physical size of the wetland but also on the kind of analysis, as outlined above.

1. Wetlands that occupy well-defined basins (or channels) may be the experimental units.

2. Larger or more diffuse wetlands may be better analyzed by conducting replicated studies on small plots.

3. Small basins, or cells, can be constructed within a wetland, allowing both a range of experimental treatments and replication. 

In all three approaches the most difficult decisions in establishing a study's protocol involve the trade-off between replication of treatments and establishing a spectrum of response, both within and among sites.

The following sections outline research strategies and results from several ecosystem analyses that are examples of these three approaches.