Aalto's primary research interest is theoretical fisheries ecology, with a focus on population dynamics, spatial dynamics, and response to disease and catastrophic events. His current work involves the incorporation of the effects of ocean acidification and low-oxygen events into an abalone growth and reproduction model. Past projects include modeling indirect positive effects from fishing-induced competitive release, effects of size-specific obligate predation on post-harvest recovery time, and assessing the decline and current state of European eel fisheries.