In short, yes. In addition to the big campaigns you hear about in Virginia and Tennessee, there were a lot of more minor operations going on in other theaters. Several of those were amphibious operations.

Now, they really weren't opposed landings, D-Day style coming ashore from ships against enemy resistance. The technology really wasn't there, or the need--the South has an exceptionally long coastline and not enough troops to garrison the entire thing. There were attempts at opposed crossings of rivers using pontoon bridges and assault boats--for example, the crossing of the Rappahannock at Fredericksburg under fire from Barksdale's men--but I imagine that's not the kind of thing you're asking about.

I'll start with a big one. McClellan's Peninsula Campaign in 1862 was an amphibious operation, aimed at outflanking the Confederate river-based positions. Initially, Johnston's army was dug in on the Potomac, and McClellan proposed an amphibious landing at Urbana in order to put the Union Army between Johnston and Richmond. Before the plan went into action, however, Johnston withdrew from the Potomac to the Rappahannock, rendering that plan moot--so McClellan revised the operation into a landing at Fort Munroe at the end of the peninsula between the York and James Rivers. Now, Fort Munroe was in Union hands, and had been since the start of the war--but McClellan had used naval transport to shift his army around the flank of the Confederate defenders, and place his army behind enemy lines, as it were. In that he was successful--Johnston had to rush back to defend Richmond--but Magruder (the Confederate commander in charge of the fort at Yorktown and other Confederate forces bottling up the Union forces in Fort Munroe) made his forces look far larger than they actually were, and McClellan, with his characteristic cautiousness, fell for it completely and bought time for Johnston to redeploy his army to the peninsula. The campaign did come close to taking Richmond--closer than the Union would until 1864, as far as I know--but due to (again) McClellan's trademark over-caution and the arrival of two folks by the name of Robert E. Lee and Stonewall Jackson forced McClellan to abandon the campaign.

You might be familiar with the "Anaconda Strategy." This was the overall plan for conducting the war spearheaded by Winfield Scott in the early days of the conflict. The general idea was to put the South into a stranglehold, by cutting off access to the sea, cutting off the Mississippi River, and exerting pressure from all sides. Part of this strategy was the Union blockade, but the Confederates held many of the forts built before the war to guard many of the harbors in the South. These forced Union blockading forces to stand off from Confederate harbors, weakening the blockades, and many of the Union amphibious operations were aimed at seizing these forts. Generally Union forces would land nearby and make the assault overland, often with support from blockading ships. One such attack was the subject of the end of the movie Glory, the (second) assault on Fort Wagner, which was one of the fortresses guarding Charleston Harbor. This assault failed (as well as the first, it goes without saying), although operations against the Charleston fortifications continued. Fort Wagner eventually was abandoned and occupied by Union forces.

In 1862, Burnside (famous for his participation at Antietam/Sharpsburg--a bit unfairly imo--and infamous for his mishandling of Fredericksburg) led an expedition in Eastern North Carolina, which resulted in the Union seizing many of the forts around the various North Carolina waterways and overall shutting down those routes to Confederate blockade runners.

One thing to consider, though, is that while the Confederates could not challenge Union naval superiority, they could prevent the Union from projecting naval power locally--or at least threaten Union transport or supply ships. For example, during the Peninsula campaign, the CSS Virginia was still active and threatening Union moves up the James River, as well as Confederate forts such as the aforementioned one at Yorktown. This is why McClellan had to land so far down the peninsula, and Union ground forces had to reduce such fortifications in order to allow ships with supplies to reach Union forces. Incidentally, another naval operation was able to take Norfolk--CSS Virginia's home port--which forced the Virginia was forced upriver and eventually scuttled.

So to summarize, the Union did utilize small-scale amphibious assaults all along the Confederate coast in order to cut off Confederate access to the sea. Larger scale operations, such as McClellan's peninsula campaign, were attempted, but there were logistical issues in keeping such a force supplied by sea, which mostly limited the operations to smaller-scale efforts.