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There are a lot of stories in the NYC subway whose theme is "plus ca change," but I really don't think anything can beat Dekalb Avenue for such consistent troublemaking.
The junction and associated stations were built in stages from the early 1910s until 1920, when the Montague St tunnel opened, becoming the nexus of the BMT's subway network.
While it's import to the subway is nothing to be scoffed at today, it was even more so back then. Not only was subway ridership in South Brooklyn generally higher in the 20s, 30s and 40s, but Dekalb was also just responsible for Manhattan access in more of Brooklyn.
Dekalb Avenue provided Manhattan-bound trains on the Culver line below Ditmas Avenue until 1954 (grey), and, until the the IND opened to Church Avenue in the 30s, its trains were simply the only Manhattan-bound game in town south of the IRT (blue).
(The BMT did run el service to Park Row until the '40s, but a) that service was ~useless as Lower Manh shifted southwards/employment went to Midtown, and b) in later years, through service from S. Bk via 5 Av el was unavailable. A svc guide from '39, showing 5 Av el to Sands St:)
Alas, the junction was, from the get go, a dysfunctional mess. Cramming trains from 7 track pairs on the Brooklyn branches into 3 as they approached/transited Dekalb is hard enough to begin with, but the paths trains took through the interlocking made the task ~impossible.
The interlocking's reliance on flat crossovers to sort trains between entry and exit points was the crux of the issue. Trains were forced to cross and merge in front of each other at numerous points throughout the interlocking, which wrecked reliability and capacity.
Of course, there were ways to simplify movements through that interlocking, but that was hardly the BMT's (or NYCTs) ethos. This map by @transbay gives an excellent sense for the sheer number of service permutations Dekalb had to handle at one time.
transbayblog.com/new-york-city-…
(Small digression: southbound trains coming out of the Tunnel into Dekalb could have taken one of three routes at those switches (bypass, Brighton, 4th local), which required a creative signalling solution given NYCT/BMT signals can only efficiently provide for up to 2 routes)
(The fix was adding a blue indication to the normal green/yellow/red, which led to these routes. If you need to brush up on how to read route signals, have a look here:)
nycsubway.org/wiki/Subway_Si…
Dekalb's issues were noted almost as soon as the complex opened. This report from 1924 notes how the junction's design (as well as that of surrounding segments) made achieving full capacity difficult.

nycsubway.org/wiki/Transit_T…
Hoping to fix the problem by providing more capacity in Manhattan, its solution was completing one of the BMT's planned loops.
Before 1967, the south tracks on the Manh. Bridge went to Chambers, and the northern pair to Broadway. However, it was not until 1931 that the Nassau St line opened south of Chambers , which meant everything on the south side ended at Chambers. (Map h/t nycsubway.org)
It was the completion of that segment, which would connect to the Montague St Tunnel and allow trains to pass through Broad, Fulton and Chambers before heading back to Brooklyn, that was being advocated for in the document--it made the bridge-Nassau connection more useful.
The story of the loop is important context for some of the larger planning issues with Dekalb's network. While in the purest of operational senses, it wouldn't have mattered whether the south side of the bridge was a direct express to Fresh Kills...
...the fact that only one of the three track pairs heading north out of Dekalb (the north side of the Bridge, which became Broadway express) went to Midtown became an increasingly important issue as employment migrated north.
While the Montague tunnel was useful insofar as it provided the quickest route to the lower end of Lower Manh., the bridge's south tracks became a rush hours only concern (an imbalance which was so pronounced for so many years that it caused structural issues for the Bridge)
This infrastructural underuse is what gave us Chrystie St. Among other things, that project disconnected the Nassau Loop from the Bridge, shifting Broadway trains to the south side and using the north to link up with 6th Avenue via Grand St (map h/t @vanshnook)
With $ available and more svc needed, planners decided to do fix the abhorrent layout at Dekalb. By closing Myrtle, shifting the Dekalb platforms, and rearranging Brighton, they made it possible to use almost any route through the area without crossing in front of another train.
This was very exciting for planners; back then, service pattern complexity was not a dirty phrase. They came up with this service plan (some call it "no switch left behind") which would have fully flexed Dekalb, as well as another junction at 36 St on 4th Avenue.
(That wasn't what they ended up implementing, though the final service plan was hardly lacking in complexity; the only route not used was 4th local to Manhattan Bridge)
Part of the reconstruction (which took place from ~1956-1960) was installing a new dispatching system to control movements through the area. This machine was capable of seeing trains' route selections at Canal/Grand and having those selections track with them over the bridge.
Theoretically, this would allow for automated, fluid ops where trains chose a routing at entry stations and moved fluidly through to exits. Keep this capability in mind for later -- the system controlling the interlocking today is the same as was installed in the 50s.
After the opening of Chrystie St, Dekalb, much like the rest of the system, went into decline. First, service cuts reduced train volume, and then endless work to correct structural issues on the Manhattan Bridge closed alternating routes over a span of about twenty years.
It was only in 2004 that the interlocking was restored to full service, using the same service pattern as today, except back then the M still ran to South Brooklyn.
However, Dekalb of today is not the Dekalb that was rebuilt in the 1950s. Few areas were harder hit by signal modifications than the interlocking, changes which have palpably reduced capacity and increased delays.
Additionally, thanks to reliability issues with the train identification system (really, the issue is operators accidentally selecting the wrong route through), Dekalb was equipped with a set of CCTV cameras in the 1990s.
This means that now, many trains have to stop in the middle of the interlocking so that someone in the tower can double check their identity before issuing a route through. Needless to say, this is a slow, inefficient process. Luckily, it seems (?) to be on the wane.
And then, of course, there is the undergirding issue with the area: merges. Dekalb sorts trains for the 4th avenue express tracks and the Brighton line. It does so downstream of at least one other merge in every case (increasing the likelihood of off-schedule arrivals)...
...and at low speed. Combined with the previous two issues, and the related problems of the Manhattan Bridge crossing, the Dekalb-Manhattan segment on each route sticks out like a sore thumb on variability plots.
While the junction affords riders a choice of routes and easier transfers, Broadway and 6th Avenue run less than a block apart in Midtown; the only stops with significant distance between them are W4 and USQ, and in the case of USQ a 6th avenue rider can catch the 6.
To increase reliability/capacity through the junction -- not just for the sake of South Brooklyn, but also for the sake of folks indirectly affected by the interlocking's nuttiness, for example on CPW -- I'd argue we should deinterline the area.
For the sake of weekend service simplicity, I'd advocate for B/D to Brighton and N/Q to 4th, but this is obviously something worth committing the resources for a ridership study and one for potentially facilitative capital investments.
While not so much an operational fix, the subway generally could benefit from making more use of capacity in the Montague St tunnel. Back in the '70s, the tube carried nearly as many people into Lower Manhattan during the peak as the Lex. Today, not so much.
While peak hour volumes to Lower Manhattan are down overall, crowding on the lower end of the Lex remains strong as people transfer onto it at Fulton to reach East Midtown/USQ. Drawing riders to Montague could be a cheap way to ease the problem.
I would in fact argue that the largest problem facing Dekalb today isn't even its merge and signal frustrations, but its underuse. We have a piece of infrastructure potentially capable of handling 90+ trains per hour from South Brooklyn into Manhattan; we run 50.
In the short run, especially if the consensus after COVID dictates a new focus on crowd reduction, we should seek to up that figure to attract riders. In the long run, it could enable massive upzoning in South Brooklyn with little to no need for additional infra investment
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