Removing fork.

http://matome.naver.jp/odai/2139047452537935301
http://kotobank.jp/word/かいぼり
http://portal.nifty.com/kiji/140205163203_1.htm

I'm a little unsure how you went from your dictionary 
definitions to thinking that "to catch fish" is the 
_primary_ aim of the practice. For example, why would it be 
referred to as an "agricultural practice" and consistently 
mention "drying out the floor of the lake under the sun"? 
These things have nothing to do with catching fish. Every 
dictionary/encyclopedia source you mention, plus my 
contemporary journalistic sources (5 now), mention many 
purposes other than "catching fish". 

This part of Wikipedia is especially telling:
農業用のため池を維持するために行われてきた伝統的な管理方法で
ある。稲作が終わる晩秋から早春にかけての農閑期に、池の水を抜
き天日に干し、堆積したヘドロや土砂を取り除いて肥料にし、獲っ
た魚を利用してきた。
栄養塩類を含んだ泥や水を排出し、また池の底を空気にさらして微
生物による分解を促進することで、水質を浄化する効果がある[3]
[4]。
農業目的の他に、水質改善や外来生物駆除のための掻い掘りが各地
で行われている[5]。

This is an *agricultural practice*　(農業＝土地を利用して作
物を栽培し、また家畜を飼育して衣食住に必要な資材を生産する産
業。広義には農産加工・林業も含む), not a fishing practice. 
Although catching fish is certainly part of what is done, it 
is by no means the sole or main purpose of the practice.

gg5, koj, daij, etc.

the key is that it is usually done to catch fish.  AFAICT, the reference provided doesn't suggest that there's anything particularly unusual about the procedure, just that it is traditional

@@ -5,0 +6,3 @@
+</k_ele>
+<k_ele>
+<keb>搔い掘り</keb>
@@ -13,2 +16,6 @@
-<gloss>drain a lake or pond</gloss>
-<gloss>a traditional agricultural practice of draining ponds</gloss>
+<gloss>draining a pond, lake, or ditch (to catch fish)</gloss>
+</sense>
+<sense>
+<pos>&n;</pos>
+<pos>&vs;</pos>
+<gloss>cleaning a well</gloss>

http://www.japantimes.co.jp/news/2014/04/08/national/war-on-
invasive-species-continues/#.U0SY96h_uSo

The current entry seems rather inadequate, as though 
"kaibori" is just a normal old word meaning to drain a 
lake/pond. In reality, it is a semi-untranslatable cultural 
practice, and I have quoted the article's definition as a 
supplement to the current entry.

@@ -13,0 +14 @@
+<gloss>a traditional agricultural practice of draining ponds</gloss>

All Japanese dictionaries (and Japanese Wikipedia) disagree.  It is specifically about "catching fish", which the edited version above omits.  "Catching fish" does not necessarily suggest you're taking them to eat them; one can "catch fish" for removal as well.

For instance, Kojien:
池・沼などの水を汲み出して干し、中の魚を捕ること。また、「井戸さらえ」にもいう。
Daijirin:
池や沼の水をくみ出して干し，魚をとること。
Wikipedia:
掻い掘り（かいぼり）は、池や沼の水をくみ出して泥をさらい、魚などの生物を獲り、天日に干すことである。

Rejecting this branch, as you forked the entry.
If responding to a comment, respond to that entry, not to the original, as when an entry has been forked it cannot be approved.  I will change the wording on the other branch.

http://www.city.mitaka.tokyo.jp/c_service/043/043944.html

Sorry, it's not really "to catch fish," as the point is to 
kill the fish for the good of the ecosystem and purify the 
lake water of contaminants. "To catch fish" implies that the 
point is to catch the fish for food, and that just isn't 
accurate in modern usage. Every modern Japanese article on 
this topic even says the purpose of the practice is 水質改
善, which again has nothing to do with "catching fish".

The reason the JT article and others use the phrase 
"kaibori" is for precisely the same reasons you would use 
any other romanized Japanese phrase in English: because it's 
a traditional practice and merely calling it "lake-draining" 
would ignore the centuries of history behind it.

http://www.japantimes.co.jp/news/2014/04/08/national/war-on-
invasive-species-continues/#.U0SY96h_uSo

The current entry seems rather inadequate, as though 
"kaibori" is just a normal old word meaning to drain a 
lake/pond. In reality, it is a semi-untranslatable cultural 
practice, and I have quoted the article's definition as a 
supplement to the current entry.

@@ -13,0 +14 @@
+<gloss>a traditional agricultural practice of draining ponds</gloss>