Hereditary Spastic Paraplegias (HSPs) comprise a diverse set of genetic diseases caused by mutations in any of up to 70 genes, named SPG1 to SPG72. Age-dependent corticospinal axon degeneration, accompanied by spasticity and weakening of the lower limbs, represents the most prominent HSP clinical feature. Two genes implicated in HSPs encode proteins that regulate ER morphology. Atlastin (responsible for SPG3A), encodes an ER membrane GTPase responsible for the fusion of juxtaposed ER membranes, and Reticulon 2 (responsible for SPG12), inserts into the ER membrane, induces membrane curvature, and thus promotes ER tube formation. Here we describe the effects of altered atlastin (atl) and reticulon (Rtnl1) on ER structure, evoked neurotransmitter release, synaptic bouton formation (arborization), and locomotor behavior in Drosophila. Using a novel fluorescent ER marker, we show that the ER within wildtype motor nerve terminals forms an elaborate network of tubules that resembles a “basket”, but this network is fragmented and diffuse in larvae lacking atl. Additionally, we find that loss of atl or Rtnl1 decreases evoked transmitter release from motor neurons and increases motor neuron arborization. We also find that atl acts cell autonomously in the motor neuron to affect transmitter release, whereas Rtnl1 acts in all three cell types (neuron, muscle, and peripheral glia) of the tripartite synapse to control transmitter release. Similarly to other HSP genes, atl inhibits bone morphogenetic protein (BMP) signaling, and loss of atl causes age-dependent locomotor deficits in adults. These results demonstrate a critical role for the ER in neuronal function and identify mechanistic links between ER morphology, neuronal structure and function, BMP signaling, and adult behavior. These studies provide novel insights into the mechanisms underlying the neurological deficits in these HSPs.