Seagrass meadows are vital coastal ecosystems that support fish and prawn assemblages, providing essential resources such as food and refuge. They are especially important as nursery habitats for ecologically and economically important juvenile fish and prawns. However, seagrass ecosystems are declining globally due to their vulnerability to both natural disturbances and anthropogenic impacts. Effective monitoring and management strategies are therefore essential to ensure their conservation and ecological functionality. This review synthesises literature on methods for sampling fish and prawns in seagrass habitats, grouping them into three categories: capture, sensory, and molecular approaches. Capture methods, including beam trawls and seine nets, provide valuable biological data, but are extractive and can be destructive to the surrounding habitat. Sensory methods such as baited remote underwater video systems (BRUVs) and hydroacoustic techniques, offer a non-destructive alternative, but can be negatively influenced by environmental conditions such as turbidity and habitat complexity that are common in seagrass meadows. Molecular approaches, particularly environmental DNA (eDNA) metabarcoding, present a highly sensitive and non-invasive alternative approach, but challenges remain in quantifying species abundance and demographics. To guide method selection, we propose a structured framework of questions and visualisations to assist researchers in selecting the most appropriate sampling methods based on their specific research objectives. Given the biases and limitation of these methods individually, we suggest integrating multiple methods to enhance assessments of marine communities in seagrass habitats. Future research should focus on refining these methodologies to improve the accuracy of biodiversity monitoring in seagrass meadows, whilst minimising environmental impacts.