The burrowing shrimp Neotrypaea californiensis is an important ecosystem engineer that inhabits estuaries along the US Pacific Northwest coast. This species plays an important role in the estuarine ecosystem but negatively impacts oyster aquaculture through its burrowing activities. Development of population models for burrowing shrimp management requires more detailed life history information and accurate estimates of age. Ageing studies have been limited for crustaceans because it is generally believed that they do not retain structures with annual deposits commonly used to age other marine organisms, when they moult their exoskeletons. A mesocosm growth experiment and field surveys were combined to compare the performance of two ageing techniques, quantification of autofluorescent lipofuscin and gastric mill ossicular lamellae, for estimating age in N. californiensis. Animals of known age were grown in outdoor mesocosms and sampled regularly to correlate age metrics with body size and true age. Lipofuscin concentration increased with time across multiple cohorts at the rate of 1.430 ± 0.060 ng µg−1 year−1. Lamellae counts also increased with time (4.922 ± 0.337 lamellae year−1). While age estimates based on lipofuscin concentration and lamellae counts generally agreed, carapace size did not correlate to either age metric. Lamellae counts from field collections suggest they are added sequentially with age but the relationship can vary by location. When used together, the application of both techniques may provide robust estimates of crustacean age especially when size-based measurements are imprecise.