One thing that I wanted to include in my layout from the onset, even before I made the choice between HO and N scale, was a creek.  It would add some interest, and some variation and bridges to an otherwise flat "tabletop" type of layout (which was one of the possibilities at the time).  But even a mountainous layout, which I ended up with, a creek expands the "depth" of the scene.
As plans are right now, the creek will be one of the last items I take care of.  I will be making another small test diorama to try out and perfect my methods of creating the creek, including debris, rocks, and bankside foliage.
Before any creek-bed or banks were built, I installed the bridges.  The girders and ballasted decks of those bridges were Micro-Engineering kits.  For some, I kept them at the 40' length, while others I shortened to match the area.  I then used styrene and putty to build up the concrete foundations on each end, and then installed them under the existing track.  For the bridge near switch for the Blue Creek spur I cut the two ballast decks at an angle, and joined them just beyond where the frog of the switch is located.  I then built appropriate concrete foundations out of styrene, painted them, inserted the steel girders, and installed the bridge under the tracks (which were already installed).
 
For the truss bridge, I had originally purchased a Kato through truss, and intended to shorten it to fit the space.  The problem was that the Kato bridge is very tall, and sticks out like a sore thumb amongst everything else in the layout.  So I then purchased a pair of Atlas through truss bridges.  First, I installed the Micro-Engineering code 55 bridge flex track.  Then, I added Micro-Engineering code 40 rail for guardrails (as I did on every bridge), and painted the track.  I then cut the center track out of each bridge, and then kitbashed two sides to make one long side to match the desired bridge length.  I then cut some styrene I-beams to span the width of the bridge, so that the two sides can tie into the track and support it.  I then made some simple concrete foundations out of styrene, and mounted them under the bridge.
 
The last bridge installed was the small wood trestle leading to Mine #2.  It is a modification of a Blair-Line kit.  For this bridge, built a foundation out of styrene that matched the profile of the plywood subframe.  I then took the styrene foundation from the layout, and built the trestle kit on it.  Once that was done and painted, I installed the assembly back onto the layout.  I then took some Micro-Engineering Code 40 flextrack, and cut the plastic ties so that they were separate from each other.  I then temporarily placed the flextrack over the area, and secured it with push pins, and marked the rails where the bridge was.  I removed the flextrack, and then spaced the ties over the bridge section as close as the other bridge flextrack.  I then separated the ties over the rest of the track to the width of the Peco track (like I did with the other code 40 flextrack on the layout).  I then reinstalled the flextrack, checked to make sure things were aligned properly, and glued the track to the roadbed and bridge.  There is a severe dip from the turnout down to the bridge itself, but it represents an awkward, rickety type of spur.
Once all of the bridges were in place, I used wood filler to make the creek banks because it fills gaps between subroadbed boards better than spackling compound, and without needing any other support.  I didn't sand everything smooth, I only "knocked" off severe high spots and points, and kept the texture for a more natural look.  Then the banks were painted when ground cover was applied to the rest of the layout.