Increasing international maritime transport drives the need for efficient container terminals. The speed at which containers can be processed through a terminal is an important performance indicator. In particular, the productivity of the quay cranes (QCs) determines the performance of a container terminal; hence QC scheduling has received considerable attention. This article develops a comprehensive model to represent the waterside operations of a container terminal. Waterside operations comprise single and twinlift handling of containers by QCs, automated guided vehi- cles and yard cranes. In common practice, an uncoordinated scheduling heuristic is used to dispatch the equipment operating on a terminal. Here, uncoordinated means that the different machines that operate in the container terminal seek optimal productivity solely considering their own respective stage. By contrast, our model provides a coordinated schedule in which operations of all terminal equipment can be considered at once to achieve productivity closer to the QC optimal. The model takes the form of a hybrid flow shop (HFS) with novel features for bi-directional flows and job pairing. The former enables jobs to move freely through the HFS in both directions; the latter constrains certain jobs to be performed simultaneously by a single machine. We solve the coordinated model by means of a tailored simulated annealing (SA) algorithm that balances solution quality and computational time. We empirically study time-bounded variants of SA and compare them with a branch- and-bound algorithm. We show that our approach can produce coordinated sched- ules for a terminal with up to eight QCs in near real time.