A basic property of any diffusion-based molecular communication system is the geometry of the enclosing container. In particular, the geometry influences the system's behavior near the boundary and in all existing modulation schemes governs receiver design. However, it is not always straightforward to characterize the geometry of the system. This is particularly the case when the molecular communication system operates in scenarios where the geometry may be complex or dynamic. In this paper, we propose a new scheme-called equilibrium signaling-which is robust to uncertainties in the geometry of the fluid boundary. In particular, receiver design only depends on the relative volumes of the transmitter or receiver, and the entire container. Our scheme relies on reversible reactions in the transmitter and the receiver, which ensure the existence of an equilibrium state into which information is encoded. In this case, we derive near optimal detection rules and develop a simple and effective estimation method to obtain the container volume. We also show that equilibrium signaling can outperform classical modulation schemes, such as concentration shift keying, under practical sampling constraints imposed by biological oscillators.