Knowledge of macrophytes and macroinvertebrates composition in a changing environment is essential for wetland monitoring. This paper assesses the biodiversity in two wetlands of different trophic levels in the Bamenda town at three different stations. Macrophytes and macroinvertebrates diversities were assessed respectively through Braun-Blanquet and multi-habitat approaches. The water physico-chemistry of these wetlands was also determined following standard protocols for water analysis. Based on the water quality, the principal correspondence analysis showed that station 3 stands out from the others with high organic and mineral parameters. A total of 19 families of macrophytes belonging to 35 genera and 42 species were identified. The Shannon –weaver’s Diversity index varies from 2.48 (station 2) to 1.90 (station 3) indicating a reduction of the plant diversity with the increase of human pollution. The dominant and common species identified in the study sites are: Alternanthera sessilis, Commelina benghalensis, Echinochloa pyramidalis and Pennisetum pupureum. These species tolerate the organic pollution, and could be used in the context of bio-purification of wastewater. Concerning macroinvertebrates, they belong to 1 phylum, 4 classes, 9 orders, 35 families and 55 genera. The most abundant class was the insects with 97% of the total fauna followed by the class Annelids which represented 3%. The abundant family was Gerridae represented by 7 genera. A negative correlation was found between water pollution and biodiversity meanwhile a positive correlation was found between macrophytes presence and macroinvertebrate diversity.