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Island nations such as New Zealand provide valuable insights into conservation challenges posed by strongly connected and recently developed or exploited freshwater and marine ecosystems. The narrow land mass, high rainfall, and steep terrain of New Zealand, like many other island nations, mean that land-based stressors are rapidly transferred to freshwater habitats and propagated downstream to coastal environments via short, fast-flowing river systems. Freshwater and marine environments are linked through faunal life histories; for example, diadromous fishes, many of which are considered threatened or at risk of extinction, and require cross-ecosystem conservation to ensure survival of critical life stages and persistence of source populations. Recent invasions of marine and freshwater environments by non-indigenous species reveal rapid impacts on a naive biota and highlight conservation conundrums caused by management aimed at enhancing native biodiversity by improving habitat connectivity. Understanding and managing interconnected freshwater and marine ecosystems is a key concept for local indigenous communities, and highlights socio-cultural connectivity and sustainable local harvesting of traditional resources as key elements of contemporary marine and freshwater conservation planning in New Zealand.