Aquatic species represent a vast diversity of metazoans, provide humans with the most abundant animal protein source, and are of increasing conservation concern, yet landscape genomics is dominated by research in terrestrial systems. We provide researchers with a roadmap to plan aquatic landscape genomics projects by aggregating spatial and software resources and offering recommendations from sampling to data production and analyses, while cautioning against analytical pitfalls. Given the unique properties of water, we discuss the importance of considering freshwater system structure and marine abiotic properties when assessing genetic diversity, population connectivity, and signals of natural selection. When possible, genomic datasets should be parsed into neutral, adaptive, and sex-linked datasets to generate the most accurate inferences of eco-evolutionary processes. Proliferation of genome-scale studies on aquatic species have resulted from the decreasing costs of high-throughput sequencing combined with novel computational approaches. Our increasing understanding of the genomes of aquatic species has enabled the annotation of loci that are adaptive, sex linked, and associated with phenotype, allowing the inference of evolutionary and demo-genetic processes from spatio-temporal genetic patterns. Recent improvements in climate and habitat data for aquatic systems provide a more precise characterization of aquatic niches, facilitating landscape genomics. Many landscape genetic analytical methods have recently been developed specifically for aquatic systems. We provide a list of spatial and genomic resources as part of a ‘roadmap’ to guide future aquatic landscape genomic studies.