Understanding whether natural populations will be able to adapt to selective pressures associated with rapid environmental and climatic change is a research priority. Measuring the strength and characteristics of selection in natural populations remains a daunting task, particularly for non-model species. In this talk I present results (and several unresolved challenges) from three research programs that study adaptation in non-model marine and freshwater organisms by integrating population genomics with environmental modelling and common-garden experiments. Each program explores natural replicates of the adaptation process by comparing closely related lineages and populations in geographically separate environments or in shared environments. Our datasets include ddRAD, RNA-seq, candidate adaptive genes, habitat mapping and trait phenotyping. The main aim of the first program (23 populations of two species of abalones, n=732) was to assess the relative contributions of space and selection in large, well-connected marine populations. Substantial neutral gene flow was the norm in both species, but their adaptive datasets showed marked population structure associated with environmental heterogeneity; in particular, with thermal gradients. In the second program (50 populations of two perch species, n=638), we tested for associations between neutral and adaptive diversity and gradients of environmental disturbance. Both species showed neutral population structure linked to the riverine network. However, it appears that long-term environmental instability (measured by natural hydroclimatic disturbance) has promoted adaptive diversity and evolutionary resilience in these lineages. In the third program (39 riverine populations of two rainbowfish species, n=1035) we experimentally assessed adaptive potential to climate change and tested landscape predictions from the 'climatic variability hypothesis'. We showed heritability and heritable plasticity for the expression of candidate genes in future climates. At a landscape level, populations from more variable habitats showed higher adaptive resilience to climate change. Strategies for cataloguing adaptive resilience to environmental change in ecologically important organisms are discussed.