We study the dynamics of quantum systems interacting with a stream of entangled qubits. Under fairly general conditions, we present a detailed framework describing the conditional dynamical maps for the system, called quantum trajectories, when the qubits are measured. Depending on the measurement basis, these quantum trajectories can be jump-type or diffusive-type, and they can exhibit features not present with quantum optical and single-qubit trajectories. As an example, we consider the case of two remote atoms, where jump-type quantum trajectories herald the birth and death of entanglement.