For animals that live in a reasonably variable environment the capacity for learning and memory allow them to adapt to the changes they experience. Ecological factors that vary between habitats can affect a range of learning behaviours. Less attention has been directed at how this variation may affect memory processes, or how different ecological variables might interact when shaping cognition and behaviour. Therefore one aim of this thesis was to investigate how different ecological variables shape memory abilities and to test whether those same variables affect other related behaviours such as learning. In order to test this, I selected natural populations of a temperate freshwater fish, the three-spined stickleback (Gasterosteus aculeatus) from pond and river habitats that were proposed to differ in predation pressure, and assayed their learning, memory and other behavioural traits. Pond and river populations differed in their memory and orientation behaviour. An interaction between pond/river habitat and predation pressure affected learning rate, and a similar interaction affected temperament behaviours. Two further studies were conducted to address how captive rearing environments and typical handling procedures affect behaviour in different species. Rearing environment affected memory, but not learning or temperament behaviours in three-spined sticklebacks. Handling caused stress responses in three-spined sticklebacks, Panamanian bishops (Brachyraphis episcopi) and Rainbow trout (Oncorhynchus mykiss), but handling with a water filled scoop compared to a traditional dip-net decreased these responses in three-spined sticklebacks and Panamanian bishops, and also affected behaviour in Panamanian bishops. The results presented in this thesis suggest that ecological variables play a substantial role in shaping learning, memory and other behavioural traits in fish, and highlight the utility of behavioural assays in answering welfare-based questions.