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The district has a network of rivers,canals and backwaters. Manimala, Pampa and Achancovil are the major rivers.
It originates from Mothavara hills in Kottayam district enters the district at Thalavadi village in Kuttanad taluk and passes through Edathua and Champakulam villages and joins the Pamba river at Muttar.The villages of Manimala, Mallappally, Kaviyoor, Kalloppara, Thalavadi, Kozhimukku and Champakkulam lie in the course of the river Manimala. It has a length of 91.73 Km and drainage area of 802.90 Km.
Pamba, the third longest river in Kerala is formed by several streams originating from Peerumedu plateau in Idukki district, enters Alappuzha district at Chengannur and flows through Pandanad, Veeyapuram, Thakazhy, and Champakulam through a distance 177.08 Km and plunges into vembanad lake through several branches such as Pallathuruthi Ar, Nedumudi Ar and Muttar. The river has a length of 117 Km and is navigable to a length of 73 Km. The catchment area of this river is 1987.17 Sq.Km. The main tributaries of the river are Pambayar, Kakki Ar, Arudai Ar, kakkad Ar and Kallar.
This river often known as Kulallada river, originates from Pasukida mettu, Ramakkal Theri and Rishimalai of Kollam district enters the district at Venmony and has a catchment area of 1155.14 Sq.Kms and a marginable length of 32.19 Km.It passes through Cheriyanad, Puliyoor and Chengannur villages, enters Mavelikkara Taluk at Chennithala, flows through Thriperumthura and pallippad villages and joins Pamba at Veeyapuram.
The Vembanad lake, the most important of the west coast canal system has a length of 84 Km and an average breadth of 3.1 Km. It covers an area of 204 Sq.Km. Stretching from Alappuzha to Kochi it borders Cherthala, Ambalapuzha and Kuttanad Taluks of Alappuzha district, Kottayam, vaikom and Changanasserry taluks of Kottayam district, Kochi and Kanayannur Taluks of Ernakulam district. Pamba, Achankovil , Manimala, Meenachil and Muvattupuzha rivers discharge into this lake. Pathiramanal, often called the mysterious sand of midnight, having coconut palms and luxuriant vegetation is situated in the centre of this lake. Perumbalam and Pallippuram are the other islands in this lake. The Thannermukkom regulator constructed across Vembanad lake between Thannermukkom and Vechur is intended to prevent tidal action and intrusion of saline water into the lake. It is the largest mud regulator in India.
Stretching between Panmana and Karthikappally, Kayamkulam lake is a shallow lake which has an outlet to sea at Kayamkulam barrage. It has an area of 59.57 Sq.Km., a length of 30.5 Km and an average breadth of 2.4 Km. It connects Ashtamudi lake by the Chavara Panmana canal.
Alappuzha has a network of canals included in the west coast canal system which are used for navigation. The important canals are Vadai canal, Commercial canals and the link canals between these two canals. Apart from these, there are many inland canals which are mainly used for passenger navigation and commercial purposes.
The lakes are used for inland water transport of passengers and cargo. Inland fisheries have also been flourished in these regions.
Alappuzha has a flat unbroken sea coast of 82 Km in length which is 13.9 % of the total coastal line of the state. An interesting phenomenon of this seacoast during the month of June is the periodic shifting of mud bank popularly known as "Chakara" within a range of 25 Km in Alappuzha-Purakkad coast due to hydrolic pressure when the level of backwater rises during south-west monsoon.