TRIO is a high-risk gene for schizophrenia (SCZ) and autism spectrum disorder (ASD) also variants found in patients with bipolar disorder (BPD). TRIO regulates small-GTPases to control neuronal migration, synapse development and function. However, it remains unclear whether and how discrete TRIO variants differentially impact these neurodevelopmental events. Here, we use murine models to investigate heterozygous variants that impact TRIO catalytic activity and are linked to NDDs: (TRIO) +/K1431M (ASD), +/K1918X (SCZ), and +/M2145T (bipolar disorder, BPD). Heterozygosity for Trio variants impacts neurodevelopmental-associated behaviors in different ways and in some cases are selective to one sex. ASD and SCZ-linked Trio variants differentially impact head, brain, and body size in adult mice, with corresponding changes in dendritic arborization of layer 5 pyramidal neurons in motor cortex (M1 L5 PNs). Excitatory and inhibitory neurotransmission is altered in all Trio variant mice, demonstrating an E/I imbalance that is a hallmark of NDDs, coinciding with inability of +/K1431M and +/K1918X L5 PNs to undergo long-term potentiation. For the first time, we show distinct changes in glutamate release in +/K1431M and +/M2145T mice in cortical synapses, and deficiencies in the crucial presynaptic release regulators Munc18-1 and Syntaxin1a. Our work uncovers how imbalances in Rho GTPase signaling due to discrete pathogenic Trio variants underlie impaired synaptic function and NDD-associated phenotypes in mice and reveals a novel presynaptic role of Trio in glutamate release, underscoring the importance of studying discrete variants in vivo.