Hello baza. You wrote:
(I think I did it correctly but if not here goes again ) . . .
Not sure what happen in that first try - but the system says you have only made the one post, and there have been no PM's (personal messages) to me. Never mind all that as I now have received your question - and it is a bit of a controversial one!
I'm afraid I can't help with any resources relating to the early 1900's "widening" (it is really only "deepening"). I know they dynamited quite a few limestone pinnacles that were considered a shipping danger. However I assume this was fairly small scale in the scheme of things because the major dangers of Corsair & Lonsdale rocks seem to have been left pretty much intact. It is doubtful if these early episodes had any measurable effects on the tides.
The most recent "Channel Deepening Project" or "CDP" removed rock and sand on a far more "industrial scale". Although the design work started around 2004, the project was opposed by many groups with the result the dredging at the Rip didn't occur until 2008. The main targets at the Rip were removing around 3m to 5m from parts of Rip Bank and Nepean Bank along the main shipping leads. This gave a minimum depth of around 17m over a width of about 250m.
They also nibbled off a few bits & pieces offshore from Queenscliff and Portsea to achieve a minimum depth of 16m in that region. A major aspect of the project was sand dredging of some South Channel areas between Rye and McCrae to achieve a minimum depth there of 15m. There was also some significant sand/mud dredging at the north end of the Bay but I don't have any details on that.
Back to the major point of your post:
I am trying to estimate the impact those 2 events had on the average high water mark across the whole of port Phillip Bay.
The answer here is basically "not much". Although a "Greenie" at heart, at the time I was frustrated because way too much time was spent battling this project on its "increased tides" aspect, rather than the far more important long term issues of buried toxic waste, increased swell penetration, and potentially increased storm surges.
The effect of the CDP on the tides has been proved to be close to the anticipated result: high tides a little less than 1cm higher and low tides a little less than 1cm lower. The increase in tidal range is around 1%.
Common sense said this would be the likely effect of increasing the cross-sectional area of the Rip by about 1%. The image below is a bit fuzzy, but shows my checking of how much the Rip dredging would change its cross-sectional area.

Some blue wedges folk banged on about "increased tides" claiming a huge loss of foreshore area due to CDP without putting it into the proper perspective. Everyday weather effects can easily raise (or lower) the high tide levels by twenty times this amount, and up to 70 times during severe storms.
So the "increased tides" issue wasn't a big deal in my book despite much public fuss and confusion at the time. I did hear one very elderly lady getting rather upset saying "I hear the tides will be 100% higher!" (rather than 1% higher).
****** Other Effects ******As a long time boater in the Heads area I would claim that swell penetration into the Bay on the flood tide has increased significantly. In the pre-internet days we used to judge outside swell height by the clearly visible rise and fall in Bay waters while heading westward past the Quarantine Station. Nowadays you can begin to feel a big outside swell on the flood tide while passing Pt King near Sorrento (about 5km further inside the Bay.)
As far as higher storm surges goes I think there is evidence for this as quite a number of 50+ year old beach boxes from Rye to Mt Martha have been undermined and collapsed since the CDP. Some low lying areas on the Bellarine Peninsula also seem to have experienced more frequent and higher inundation levels. Some will claim it is climate change rather than CDP.
Sea level rise itself is currently running at about 2.4cm per decade, so that in itself is unlikely to be the cause. More frequent and or more intense storms might be a possibility. It seems the only way to differentiate between climate change and the CDP is to look at the time-scale of any increase of storm surges. We might expect any increase to be gradual over time if climate change is the cause, but more suddenly after 2008 if it is a CDP effect.
The CDP planning process had experts claiming any increase in storm surge height would be minimal and only detectable by "sensitive instruments". This claim is based on the fact that although the Heads are narrow, they do not offer any protection from storm surges entering from Bass Strait. This is because the time scale of storm surges is several times longer than that of the normal tides. This means the surges aren't "filtered" by the Heads and will come through at almost 100%, regardless of any small changes made by dredging. Note the faster changing tides are reduced by around 40% in height when they come through the Heads.
This is a perfectly valid argument that I do accept, even though I have the "feel" of higher surge levels at my local beaches. (More erosion, more frequent "zero freeboard" at the local boat ramp jetty, completely "drowned beaches" more often, etc.) Maybe there is some other effect in operation such as the combination of swell penetration and storm surge that delivers higher water levels to places well beyond the reach of the swell alone. The quote below is from an old "Dive-Oz" post (2016) of mine on this topic.
The "trigger level" for serious beach erosion in my area seems to be when the Hovell Pile tide gauge off Rosebud reaches a reading of 1.5m or more. This gauge has been in operation for 25 years. In the 17 years before the CDP, the 1.5m level was breached three times: 1991, 2003 and 2004. On average, this was once every 5.5 years.
In the 8 years since the CDP, the 1.5m level has been breached eleven times: 2008, 2009(twice), 2011(twice), 2013, 2014(twice), 2015, and 2016(twice - so far). On average this is about once every 9 months. The strong el Nino in the winter-spring of 2015 depressed sea levels by around 10-15cm, and in doing so just saved 2015 from being another "double banger" year.
If we correct these results for the fact that the sea level itself has risen by about 0.05m during the 25 years, we get two more events in 1994, and one more in 2009 that might be regarded as "today's 1.5m equivalent". This would bring the "pre-dredge" average down to once every 3.5 years and the "post-dredge" average down to once every 8 months. By this crude measure, the significant erosion frequency seems about five times more often now.
This higher frequency does not allow the beaches to recover before the next onslaught. Several quiet years are needed before wind blown sand accumulating at the back of the beach can be colonised and stabilised by grasses.
Unfortunately I can't update that with any authority as data beyond 2015 is no longer updated. However from memory the pattern continues with the 1.5m level being exceeded at least a half-dozen times over the period from 2016 to now.
Update 17/10/2020: Well the 2015+ data did eventually get updated. The years for 1.5m+ level occurrences at Hovell Pile are: 2016 (twice), 2017, 2018 (3 times), 2019 (twice). The reason the Bay and bayside infrastructure is more susceptible to storm tides compared to areas along the ocean coast is because a big storm surge of +80cm on the ocean coast is less than half of the typical tidal range, whereas inside the Bay that same +80cm surge can double the normal tide range.
It should be noted that the Hovell Pile values mentioned earlier are all max "storm tide" heights, ie. storm tide = observed tide = predicted tide + storm surge. A proper analysis would need to separate out just the storm surge component and do a frequency analysis of surge heights both pre and post CDP, before any proper conclusions might be revealed. Unfortunately this was never done, largely because the OEM (the then Office of Environmental Monitor) spent much of its efforts comprehensively studying the "increased tides" beat-up, rather than the potentially more serious effects. (Thanks Greenies!)
So bazza while the answer to your query is "hardly any effect on the normal daily tides", you might be aware that the proposal for a new "Bay West" container port includes a much more significant dredging program. I think they are talking about 20m minimum depths and doubling the width of the Great Ship Channel at the Heads. That might be a whole different and unwelcome ball game!
cheers,
packo